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pato-ontology / pato

PATO - the Phenotype And Trait Ontology
https://pato-ontology.github.io/pato/
BSD 3-Clause "New" or "Revised" License
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Rename "proportionality to" to "ratio" #556

Closed rays22 closed 6 months ago

rays22 commented 7 months ago

of

Also, improve the textual definitions and improve the logical definitions of 'increased ratio' and 'decreased' by using EQs.

Resolve #555

sbello commented 7 months ago

I see proportionality to used in the eqs for 4 MP terms (eg.abnormal lymph node cell ratio) these have eqs in the form 'has part' some ('proportionality to' and ('characteristic of' some 'X') and (towards some Y) and ('has modifier' some abnormal)) I think ratio slots into this just fine. Most of the terms use ratio in the label already.

We aren't currently using increased or decreased child terms

The one thing that gives me pause is this part of the comment on the old term "Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right." But looking at the definition in both the old and new versions, I think the inclusion of 'the magnitude of another entity' excludes velocity since this involves a single entity.

I think the changes to the definition do not significantly alter the meaning of the term, so I am okay with this change.

ar-ibrahim commented 6 months ago

@rays22 Looks good. I just have a comment on whether the synonyms in the pattern should also reflect 'percentage' terms. For example terms like EFO:0007993 lymphocyte percentage of leukocytes describe a ratio relationship.

rays22 commented 6 months ago

@rays22 Looks good. I just have a comment on whether the synonyms in the pattern should also reflect 'percentage' terms. For example terms like EFO:0007993 lymphocyte percentage of leukocytes describe a ratio relationship.

@ar-ibrahim , In the specific case of EFO:0007993, yes, using the PATIO 'ratio' quality would be appropriate based on this part of the textual definition: ... presented as a ratio, fraction, quotient or percentage.

rays22 commented 6 months ago

Looks good except one typo.

@balhoff , Thanks for reviewing this PR and catching the typo. The typo has been fixed in https://github.com/pato-ontology/pato/pull/556/commits/ad4c591556a5a86f4b1afa15bc9dcb023460866a .